[svtoolkit-help] error in SVPreprocess.scrip
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[svtoolkit-help] error in SVPreprocess.scrip
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From: Jin S. <jin...@me...> - 2015-08-14 19:35:05
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Hi Bob,
I am using the latest version of GenomeStrip ( July21, 2015) but had the
following error message while running SV Proprocess.
"Unable to execute QScript: SVPreprocess.script() threw the following
exception: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )"
I have searched the mailing list but did not find an entry about this.
Could you let me know how to fix it? Many thanks!!
Jin
P.S. My complete error file is below:
++++++++++
Genome indexes for use with BWA are available
in /proj/seq/data on kure.
bwa/bowtie/bowtie2 indexes are located in "Sequence" directory
under the top level genome directory with name in CAPS, e.g.
MM9_UCSC
INFO 14:47:09,833 QScriptManager - Compiling 2 QScripts
INFO 14:47:17,321 QScriptManager - Compilation complete
INFO 14:47:17,438 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,438 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled
2015/05/15 09:12:56
INFO 14:47:17,438 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 14:47:17,439 HelpFormatter - For support and documentation go to
http://www.broadinstitute.org/gatk
INFO 14:47:17,439 HelpFormatter - Program Args: -S
/nas02/home/j/i/jinpengs/tools/svtoolkit//qscript/SVPreprocess.q -S
/nas02/home/j/i/jinpengs/tools/svtoolkit//qscript/SVQScript.q -gatk
/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/GenomeAnalysisTK
jar --disableJobReport -cp
/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/SVToolkit.jar:/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/GenomeAnalysisTK.jar:/nas02/home/j/i/jinpengs/tools/svtoolkit//lib/gatk/Queue.jar
-configFile /nas02/home/j/i/jinpeng
/tools/svtoolkit//conf/genstrip_parameters.txt -tempDir
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101/tmpdir -R
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.fasta
-genomeMaskFile /lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1
_v37.mask.36.fasta -ploidyMapFile
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.ploidy.map
-copyNumberMaskFile
/lustre/scr/j/i/jinpengs/GS.rmd/1000G_phase1//human_g1k_v37.gcmask.fasta
-genderMapFile /nas/depts/007/sullilab/projects/donor/bam
/donorwgs_gender.map -runDirectory
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101/ -md
/lustre/scr/j/i/jinpengs/Donor/GS/working//P1890_101//metadata
-disableGATKTraversal -useMultiStep -computeGCProfiles true -jobLogDir
/lustre/scr/j/i/jinpengs/Don
r/GS/working//P1890_101//logs -I
/nas/depts/007/sullilab/projects/donor/bam//P1890_101.clean.dedup.recal.bam
-run
INFO 14:47:17,442 HelpFormatter - Executing as
jin...@c-... on Linux 2.6.18-238.12.1.el5 amd64; Java
HotSpot(TM) 64-Bit Server VM 1.8.0_11-b12.
INFO 14:47:17,442 HelpFormatter - Date/Time: 2015/08/14 14:47:17
INFO 14:47:17,442 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,442 HelpFormatter -
----------------------------------------------------------------------
INFO 14:47:17,449 QCommandLine - Scripting SVPreprocess
INFO 14:47:17,769 QCommandLine - Done with errors
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript:
Unable to execute QScript: SVPreprocess.script() threw the following
exception: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR =
)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at
org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at
org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.RuntimeException: Cannot locate R script:
metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )
at
org.broadinstitute.sv.util.RUtilities.findRScript(RUtilities.java:47)
at SVPreprocess$PlotChrYvsChrX.<init>(SVPreprocess.q:251)
at SVPreprocess.createMakeProfilesCallGenders(SVPreprocess.q:179)
at SVPreprocess.script(SVPreprocess.q:93)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
... 10 more
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to
the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to execute QScript: SVPreprocess.script()
threw the following exception: java.lang.RuntimeException: Cannot locate
R script: metadata/plot_chr_vs_chr_readdepth.R (SV_DIR = )
##### ERROR
------------------------------------------------------------------------------------------
INFO 14:47:17,775 QCommandLine - Shutting down jobs. Please wait...
[ji
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